I realize that this is perhaps more of a conceptual issue than a practical one, but I wonder how would you deal with survey responses such as "don't know" or "not applicable." Specifically:

(1) Do you regard "don't know" and "not applicable" as missing? 

(2) If not, do you regard them as valid responses as other options (e.g., a scale of 1 to 7), and use all these values to impute missing data? That is, if someone did not answer this item, the imputed value could be don't know, not applicable, or any value from 1 to 7. If this is the correct approach, how to do it in Amelia or other software?

(3)  Is it possible to only impute the "true" missing data (i.e., not for "don't know" or "not applicable" responses), with valid responses from 1 to 7 in Amelia or other software? (Listwise removing participants who select "don't know" or "not applicable" in one variable before imputing is not a good idea because those participants may contribute to MAR/MCAR missing in other variables.)
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